hi, i want to perform complete proteasome simulation as a part of my learning my proteasome contain chain A-Z and a and b chain all things were processed successfully by renaming the generated file of chain A and B of topology and posre file because both have same name a, b and a, b renaming them to a, b and a2, b2 filename after successful run of few steps at the time of energy minimization water molecule not stable error occurs and after suffering from internet and reading same problem one person suggested that to change it into pdb and then fix the overlapping molecule manually then again covert it into gro file so then i changed it to pdb the proteasome structure got disrupted in straight lines so i thought to check form where is error started to occur in proteasome structure and all the way back to first step where we convert .pdb to .gro format with pdb2gmx command this structure error was here also this is the image of the processed proteasome in .gro file
and as soon as convert it back into .pdb format the structure becomes like this
can anyone please help me with this